Wrong system disk
I recently solved a problem for someone using Windows XP. The computer tried to load Windows but couldn’t find some files and ended up at a DOS prompt.
I watched the messages as the system booted up and noticed that it was booting from CD, checked the CD drive and sure enough there was a disk in there. Normally you would just get a non-system disk error but in this case the disk in question was actually a system disk, for Windows 98. Removing the disk solved the problem.
If you have a boot problem make sure that there are no removable disks in the drives. You can set the boot order on most computers but they often check removable drives for a boot disk before checking the C: drive.
It is amazing how often a fresh pair of eyes can spot the solution to a problem.